AMBER Archive (2001)

Subject: ADDING IONS USING EDIT

From: A.Madhumalar (malar_at_mbu.iisc.ernet.in)
Date: Sat Jul 14 2001 - 12:54:31 CDT

Dear amber users,

               When i tried to add Na+ ions using edit(AMBER5) for a
dodecamer DNA duplex i found that the two ions added were too close(at
1.311A). I want to know whether edit will check VDW contact criteria &
then add ions? Is there anyway to overcome this problem? i will be
thankful,if anybody could give me some suggestions.

madhu